What
CIC's reply makes very much sense and I am surprised at your question in the first place.
You are confused because you do not have a formal, genuine designation, else you won't be asking this question.
People don't SHOW THEMSELVES as employees OR Share holders of companies for that matter.
Either they are one of them or both - ON PAPER - formally. There is no middle ground.
I understand how things could be in India, but Canada is formal in terms of documents.
Imagine if you were in Canada, you would either have filed all of your taxes (YOUR MEANS YOU AS A PERSON) as an employee paid by a company where company retains parts of your salary as taxes and submits those annually at least to government. It also pays parts of your benefits (heath care, pension contributions etc.).
If you have been filing taxes as a self employed applicant, then you must have been paying higher taxes in some cases (no employer exists to contribute parts of your benefits). But at the same time you would have used much of your income towards COMPANY expenses (a self employed person is considered a business) and there by getting much benefit in taxes once your cash flow is above certain threshold.
The point is that at no point any one in Canada EVEN if he works at the company of his father, is in a position to CHOOSE to represent option A or B as stated earlier in the thread. Their status is predetermined based upon their past tax filings.
Ideally CIC would expect something similar to that. If you have filed your past taxes in India as a employee you should use the same - irrespective of your father being the majority stake owner / CEO or whatever.
Since things might not be same in India - try to use the one closest to your actual situation in India - have you been paying taxes as a self employed resource or have you had tax deduction as an employee.
Collect all of those docs and get those audited / verified by a 3rd party company and use their certificate